Downstream core element gene transcriptions: Difference between revisions

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{{main|Core promoter gene transcriptions|Core promoters}}
{{main|Core promoter gene transcriptions|Core promoters}}
[[Image:Preinitiation complex.png|thumb|right|250px|The diagram shows the RNA polymerase II holoenzyme attached to the DNA template strand. Credit: [[commons:User:ArneLH|ArneLH]].]]
[[Image:Preinitiation complex.png|thumb|right|250px|The diagram shows the RNA polymerase II holoenzyme attached to the DNA template strand. Credit: [[commons:User:ArneLH|ArneLH]].]]
The '''core promoter''' is the minimal portion of the [[Gene promoter|promoter]] required to properly initiate [[Draft:Gene transcriptions|gene transcription]].<ref name=Smale03>{{ cite journal
The '''core promoter''' is the minimal portion of the [[Gene promoter|promoter]] required to properly initiate [[gene transcription]].<ref name=Smale03>{{ cite journal
|author=Stephen T. Smale and James T. Kadonaga
|author=Stephen T. Smale and James T. Kadonaga
|title=The RNA Polymerase II Core Promoter
|title=The RNA Polymerase II Core Promoter

Revision as of 23:38, 13 December 2020

Editor-In-Chief: Henry A. Hoff

Template:TOCright The downstream core element (DCE) is a transcription core promoter sequence that is within the transcribed portion of a gene.

Downstream

Def. lower "down, in relation to a river or stream ... [f]ollowing the path of a river or stream"[1] is called downstream.

By analogy, gene transcription follows a path along the human DNA template strand once the RNA polymerase II holoenzyme locates the transcription start site (TSS).

Cores

Main articles: Core promoter gene transcriptions and Core promoters

Def. the "central part ... heart ... center or inner part ... [t]he most important part of a thing",[2] an "inside"[3] is called a core.

Consensus sequences

Main article: Consensus sequences

The consensus sequence for the DCE is CTTC...CTGT...AGC.[4] These three consensus elements are referred to as subelements: "SI is CTTC, SII is CTGT, and SIII is AGC."[4]

The number of nucleotides between each subelement can apparently vary down to none.

Core promoters

Main articles: Core promoter gene transcriptions and Core promoters
File:Preinitiation complex.png
The diagram shows the RNA polymerase II holoenzyme attached to the DNA template strand. Credit: ArneLH.

The core promoter is the minimal portion of the promoter required to properly initiate gene transcription.[5]

It contains a binding site for RNA polymerase (RNA polymerase I, RNA polymerase II, or RNA polymerase III).

"[T]he core promoter [consists of] the DNA sequences, which encompass the transcription start site (within about -40 and +40 [nucleotides] relative to the +1 start site"[6].

"Several factors have been identified that bind to core promoters (reviewed in Smale, 1997)"[7][8].

A core promoter that contains all three subelements of the downstream core element may be much less common than one containing only one or two.[4] "SI resides approximately from +6 to +11, SII from +16 to +21, and SIII from +30 to +34."[4]

Transcription start sites

Main articles: Start site gene transcriptions and Transcription start sites

Notation: let the subscript (+1) indicate the specific nucleobase (nucleotide) along the template strand that is a transcription start site. For example, A+1.

The transcription start site (TSS) is the location on the DNA template strand where transcription begins at the 3'-end of a gene.[9] This location corresponds to the 5'-end of the mRNA which by convention is used to designate DNA locations.[9]

Nucleotides downstream from the TSS (N+1, where N stands for any nucleotide) are numbered increasing from +1.

TSS location

One method to perform a TSS location is to test for portions of the downstream core element (DCE) within the about to be transcribed portion of the gene.

SI as 3'-CTTC-5' can occur as 3 of 4 (CTT, TTC) or 4 of 4 (CTTC). SII as 3'-CTGT-5' can also occur as 3 of 4 (CTG, TGT) or 4 of 4 (CTGT). SIII as AGC is not known to vary.

DCE SIII can function independently of SI and SII.[4]

General transcription factor II Ds

Main articles: General factor II D gene transcriptions and General transcription factor II Ds

Transcription factor II D (TFIID), a transcription factor that is part of the RNA polymerase II holoenzyme, interacts with promoters containing only SIII of the DCE suggesting a critical spacing parameter between SIII and the TATA box, initiator element, or some combination of the two.[4] TFIID probably serves as a core promoter recognition complex.[4]

TAF1 interacts with the DCE in a sequence-dependent manner.[4]

The differences between core promoters with downstream elements may be explained by

  1. "TATA- and DPE-dependent promoters are specific for particular enhancers"[4],
  2. "preferences of activators for specific core promoter architectures"[4], and
  3. "the presence of a DCE or [downstream core promoter element (DPE)] might be indicative of an architecture designed for specific regulatory networks, such as the regulation of housekeeping promoters versus tissue-specific promoters (or other highly regulated promoters) or the regulation of subsets of viral promoters."[4]

Hypotheses

Main article: Hypotheses
  1. The downstream core element is not involved in the transcription of A1BG.

Samplings

Downstream core element SIs

  1. negative strand, negative direction, looking for DCE SI: 3'-CTTC-5', 16, 3'-CTTC-5' at 81, 3'-CTTC-5' at 132, 3'-CTTC-5' at 241, 3'-CTTC-5' at 331, 3'-CTTC-5' at 367, 3'-CTTC-5' at 1555, 3'-CTTC-5' at 1655, 3'-CTTC-5' at 2557, 3'-CTTC-5' at 2595, 3'-CTTC-5' at 2730, 3'-CTTC-5' at 2811, 3'-CTTC-5' at 2828, 3'-CTTC-5' at 3407, 3'-CTTC-5' at 3610, 3'-CTTC-5' at 3909, 3'-CTTC-5' at 3936.
  2. negative strand, positive direction, looking for DCE SI: 3'-CTTC-5', 30, 3'-CTTC-5' at 456, 3'-CTTC-5' at 592, 3'-CTTC-5' at 676, 3'-CTTC-5' at 733, 3'-CTTC-5' at 760, 3'-CTTC-5' at 828, 3'-CTTC-5' at 928, 3'-CTTC-5' at 1012, 3'-CTTC-5' at 1069, 3'-CTTC-5' at 1153, 3'-CTTC-5' at 1264, 3'-CTTC-5' at 1305, 3'-CTTC-5' at 1332, 3'-CTTC-5' at 1405, 3'-CTTC-5' at 1432, 3'-CTTC-5' at 1516, 3'-CTTC-5' at 1914, 3'-CTTC-5' at 2095, 3'-CTTC-5' at 2107, 3'-CTTC-5' at 2361, 3'-CTTC-5' at 2582, 3'-CTTC-5' at 2947, 3'-CTTC-5' at 3031, 3'-CTTC-5' at 3057, 3'-CTTC-5' at 3247, 3'-CTTC-5' at 3312, 3'-CTTC-5' at 3394, 3'-CTTC-5' at 3994, 3'-CTTC-5' at 4061, 3'-CTTC-5' at 4241.
  3. positive strand, negative direction, looking for DCE SI: 3'-CTTC-5', 5, 3'-CTTC-5' at 619, 3'-CTTC-5' at 1053, 3'-CTTC-5' at 3553, 3'-CTTC-5' at 3776.
  4. positive strand, positive direction, looking for DCE SI: 3'-CTTC-5', 24, 3'-CTTC-5' at 48, 3'-CTTC-5' at 209, 3'-CTTC-5' at 232, 3'-CTTC-5' at 559, 3'-CTTC-5' at 643, 3'-CTTC-5' at 727, 3'-CTTC-5' at 768, 3'-CTTC-5' at 861, 3'-CTTC-5' at 961, 3'-CTTC-5' at 1063, 3'-CTTC-5' at 1231, 3'-CTTC-5' at 1594, 3'-CTTC-5' at 1633, 3'-CTTC-5' at 2192, 3'-CTTC-5' at 2748, 3'-CTTC-5' at 2784, 3'-CTTC-5' at 3216, 3'-CTTC-5' at 3667, 3'-CTTC-5' at 3762, 3'-CTTC-5' at 3851, 3'-CTTC-5' at 3871, 3'-CTTC-5' at 4197, 3'-CTTC-5' at 4248, 3'-CTTC-5' at 4263.

Downstream core element SIIs

  1. negative strand, negative direction, looking for DCE SII: 3'-CTGT-5', 19, 3'-CTGT-5' at 170 , 3'-CTGT-5' at 422 , 3'-CTGT-5' at 559 , 3'-CTGT-5' at 746 , 3'-CTGT-5' at 1068 , 3'-CTGT-5' at 1569 , 3'-CTGT-5' at 2015 , 3'-CTGT-5' at 2117 , 3'-CTGT-5' at 2271 , 3'-CTGT-5' at 2880 , 3'-CTGT-5' at 2948 , 3'-CTGT-5' at 3389 , 3'-CTGT-5' at 3412 , 3'-CTGT-5' at 3433 , 3'-CTGT-5' at 3756 , 3'-CTGT-5' at 4181 , 3'-CTGT-5' at 4355.
  2. negative strand, positive direction, looking for DCE SII: 3'-CTGT-5', 26, 3'-CTGT-5' at 98, 3'-CTGT-5' at 144, 3'-CTGT-5' at 264, 3'-CTGT-5' at 816, 3'-CTGT-5' at 891, 3'-CTGT-5' at 916, 3'-CTGT-5' at 991, 3'-CTGT-5' at 1729, 3'-CTGT-5' at 1860, 3'-CTGT-5' at 1998, 3'-CTGT-5' at 2074, 3'-CTGT-5' at 2182, 3'-CTGT-5' at 2250, 3'-CTGT-5' at 2260, 3'-CTGT-5' at 2308, 3'-CTGT-5' at 2342, 3'-CTGT-5' at 2925, 3'-CTGT-5' at 2931, 3'-CTGT-5' at 2957, 3'-CTGT-5' at 3349, 3'-CTGT-5' at 3390, 3'-CTGT-5' at 3434, 3'-CTGT-5' at 3617, 3'-CTGT-5' at 3622, 3'-CTGT-5' at 3640, 3'-CTGT-5' at 4392.
  3. positive strand, negative direction, looking for DCE SII: 3'-CTGT-5', 30, 3'-CTGT-5' at 394, 3'-CTGT-5' at 477, 3'-CTGT-5' at 667, 3'-CTGT-5' at 801, 3'-CTGT-5' at 919, 3'-CTGT-5' at 967, 3'-CTGT-5' at 1085, 3'-CTGT-5' at 1131, 3'-CTGT-5' at 1258, 3'-CTGT-5' at 1452, 3'-CTGT-5' at 1776, 3'-CTGT-5' at 1911, 3'-CTGT-5' at 2029, 3'-CTGT-5' at 2163, 3'-CTGT-5' at 2337, 3'-CTGT-5' at 2538, 3'-CTGT-5' at 2672, 3'-CTGT-5' at 3061, 3'-CTGT-5' at 3200, 3'-CTGT-5' at 3265, 3'-CTGT-5' at 3319, 3'-CTGT-5' at 3426, 3'-CTGT-5' at 3556, 3'-CTGT-5' at 3709, 3'-CTGT-5' at 3957, 3'-CTGT-5' at 3970, 3'-CTGT-5' at 4121, 3'-CTGT-5' at 4208, 3'-CTGT-5' at 4369, 3'-CTGT-5' at 4399.
  4. positive strand, positive direction, looking for DCE SII: 3'-CTGT-5', 15, 3'-CTGT-5' at 62, 3'-CTGT-5' at 712, 3'-CTGT-5' at 1693, 3'-CTGT-5' at 1869, 3'-CTGT-5' at 1964, 3'-CTGT-5' at 2130, 3'-CTGT-5' at 2412, 3'-CTGT-5' at 2460, 3'-CTGT-5' at 2843, 3'-CTGT-5' at 3131, 3'-CTGT-5' at 3530, 3'-CTGT-5' at 3569, 3'-CTGT-5' at 3893, 3'-CTGT-5' at 3973, 3'-CTGT-5' at 4252.

Downstream core element SIIIs

  1. negative strand, negative direction, looking for DCE SIII: 3'-AGC-5', 11, 3'-AGC-5' at 157, 3'-AGC-5' at 720, 3'-AGC-5' at 838, 3'-AGC-5' at 1065, 3'-AGC-5' at 1446, 3'-AGC-5' at 2453, 3'-AGC-5' at 2709, 3'-AGC-5' at 3501, 3'-AGC-5' at 3595, 3'-AGC-5' at 3813, 3'-AGC-5' at 4289.
  2. negative strand, positive direction, looking for DCE SIII: 3'-AGC-5', 109, 3'-AGC-5' at 64, 3'-AGC-5' at 329, 3'-AGC-5' at 335, 3'-AGC-5' at 339, 3'-AGC-5' at 383, 3'-AGC-5' at 427, 3'-AGC-5' at 431, 3'-AGC-5' at 473, 3'-AGC-5' at 511, 3'-AGC-5' at 533, 3'-AGC-5' at 560, 3'-AGC-5' at 601, 3'-AGC-5' at 613, 3'-AGC-5' at 617, 3'-AGC-5' at 623, 3'-AGC-5' at 634, 3'-AGC-5' at 644, 3'-AGC-5' at 692, 3'-AGC-5' at 718, 3'-AGC-5' at 728, 3'-AGC-5' at 769, 3'-AGC-5' at 785, 3'-AGC-5' at 831, 3'-AGC-5' at 837, 3'-AGC-5' at 853, 3'-AGC-5' at 931, 3'-AGC-5' at 937, 3'-AGC-5' at 953, 3'-AGC-5' at 1037, 3'-AGC-5' at 1054, 3'-AGC-5' at 1057, 3'-AGC-5' at 1064, 3'-AGC-5' at 1105, 3'-AGC-5' at 1112, 3'-AGC-5' at 1121, 3'-AGC-5' at 1127, 3'-AGC-5' at 1145, 3'-AGC-5' at 1205, 3'-AGC-5' at 1232, 3'-AGC-5' at 1267, 3'-AGC-5' at 1271, 3'-AGC-5' at 1288, 3'-AGC-5' at 1341, 3'-AGC-5' at 1348, 3'-AGC-5' at 1357, 3'-AGC-5' at 1363, 3'-AGC-5' at 1441, 3'-AGC-5' at 1448, 3'-AGC-5' at 1457, 3'-AGC-5' at 1463, 3'-AGC-5' at 1507, 3'-AGC-5' at 1532, 3'-AGC-5' at 1540, 3'-AGC-5' at 1595, 3'-AGC-5' at 1603, 3'-AGC-5' at 1625, 3'-AGC-5' at 1634, 3'-AGC-5' at 1678, 3'-AGC-5' at 2005, 3'-AGC-5' at 2008, 3'-AGC-5' at 2052, 3'-AGC-5' at 2102, 3'-AGC-5' at 2193, 3'-AGC-5' at 2198, 3'-AGC-5' at 2352, 3'-AGC-5' at 2390, 3'-AGC-5' at 2399, 3'-AGC-5' at 2402, 3'-AGC-5' at 2526, 3'-AGC-5' at 2536, 3'-AGC-5' at 2557, 3'-AGC-5' at 2703, 3'-AGC-5' at 2731, 3'-AGC-5' at 2749, 3'-AGC-5' at 2785, 3'-AGC-5' at 2845, 3'-AGC-5' at 2896, 3'-AGC-5' at 2970, 3'-AGC-5' at 3041, 3'-AGC-5' at 3100, 3'-AGC-5' at 3125, 3'-AGC-5' at 3137, 3'-AGC-5' at 3144, 3'-AGC-5' at 3155, 3'-AGC-5' at 3194, 3'-AGC-5' at 3211, 3'-AGC-5' at 3217, 3'-AGC-5' at 3223, 3'-AGC-5' at 3239, 3'-AGC-5' at 3262, 3'-AGC-5' at 3513, 3'-AGC-5' at 3518, 3'-AGC-5' at 3598, 3'-AGC-5' at 3668, 3'-AGC-5' at 3691, 3'-AGC-5' at 3701, 3'-AGC-5' at 3720, 3'-AGC-5' at 3723, 3'-AGC-5' at 3737, 3'-AGC-5' at 3763, 3'-AGC-5' at 3775, 3'-AGC-5' at 3808, 3'-AGC-5' at 3895, 3'-AGC-5' at 3997, 3'-AGC-5' at 4023, 3'-AGC-5' at 4026, 3'-AGC-5' at 4052, 3'-AGC-5' at 4279.
  3. positive strand, negative direction, looking for DCE DCE SIII: 3'-AGC-5', 91, 3'-AGC-5' at 35, 3'-AGC-5' at 137, 3'-AGC-5' at 146, 3'-AGC-5' at 185, 3'-AGC-5' at 403, 3'-AGC-5' at 455, 3'-AGC-5' at 500, 3'-AGC-5' at 504, 3'-AGC-5' at 540, 3'-AGC-5' at 676, 3'-AGC-5' at 728, 3'-AGC-5' at 737, 3'-AGC-5' at 778, 3'-AGC-5' at 810, 3'-AGC-5' at 870, 3'-AGC-5' at 895, 3'-AGC-5' at 909, 3'-AGC-5' at 944, 3'-AGC-5' at 976, 3'-AGC-5' at 1036, 3'-AGC-5' at 1061, 3'-AGC-5' at 1140, 3'-AGC-5' at 1194, 3'-AGC-5' at 1235, 3'-AGC-5' at 1267, 3'-AGC-5' at 1327, 3'-AGC-5' at 1367, 3'-AGC-5' at 1486, 3'-AGC-5' at 1497, 3'-AGC-5' at 1611, 3'-AGC-5' at 1678, 3'-AGC-5' at 1785, 3'-AGC-5' at 1888, 3'-AGC-5' at 1920, 3'-AGC-5' at 1969, 3'-AGC-5' at 1980, 3'-AGC-5' at 2005, 3'-AGC-5' at 2019, 3'-AGC-5' at 2094, 3'-AGC-5' at 2129, 3'-AGC-5' at 2264, 3'-AGC-5' at 2273, 3'-AGC-5' at 2314, 3'-AGC-5' at 2346, 3'-AGC-5' at 2406, 3'-AGC-5' at 2431, 3'-AGC-5' at 2472, 3'-AGC-5' at 2478, 3'-AGC-5' at 2650, 3'-AGC-5' at 2681, 3'-AGC-5' at 2741, 3'-AGC-5' at 2766, 3'-AGC-5' at 2780, 3'-AGC-5' at 2915, 3'-AGC-5' at 3032, 3'-AGC-5' at 3070, 3'-AGC-5' at 3105, 3'-AGC-5' at 3124, 3'-AGC-5' at 3177, 3'-AGC-5' at 3204, 3'-AGC-5' at 3209, 3'-AGC-5' at 3269, 3'-AGC-5' at 3294, 3'-AGC-5' at 3309, 3'-AGC-5' at 3370, 3'-AGC-5' at 3494, 3'-AGC-5' at 3646, 3'-AGC-5' at 3682, 3'-AGC-5' at 3694, 3'-AGC-5' at 3701, 3'-AGC-5' at 3726, 3'-AGC-5' at 3731, 3'-AGC-5' at 3773, 3'-AGC-5' at 3838, 3'-AGC-5' at 3845, 3'-AGC-5' at 3899, 3'-AGC-5' at 3912, 3'-AGC-5' at 4014, 3'-AGC-5' at 4033, 3'-AGC-5' at 4130, 3'-AGC-5' at 4184, 3'-AGC-5' at 4229, 3'-AGC-5' at 4261, 3'-AGC-5' at 4296, 3'-AGC-5' at 4321, 3'-AGC-5' at 4345, 3'-AGC-5' at 4411, 3'-AGC-5' at 4439.
  4. positive strand, positive direction, looking for DCE SIII: 3'-AGC-5', 26, 3'-AGC-5' at 77, 3'-AGC-5' at 457, 3'-AGC-5' at 537, 3'-AGC-5' at 593, 3'-AGC-5' at 688, 3'-AGC-5' at 761, 3'-AGC-5' at 1013, 3'-AGC-5' at 1108, 3'-AGC-5' at 1154, 3'-AGC-5' at 1181, 3'-AGC-5' at 1306, 3'-AGC-5' at 1390, 3'-AGC-5' at 1406, 3'-AGC-5' at 1490, 3'-AGC-5' at 1517, 3'-AGC-5' at 1528, 3'-AGC-5' at 1687, 3'-AGC-5' at 1713, 3'-AGC-5' at 1750, 3'-AGC-5' at 1915, 3'-AGC-5' at 1927, 3'-AGC-5' at 2091, 3'-AGC-5' at 3272, 3'-AGC-5' at 3283, 3'-AGC-5' at 3509, 3'-AGC-5' at 3985.

Downstream core element SI Complements

  1. negative strand, negative direction, looking for DCE SIc: 3'-GAAG-5', 4, 3'-GAAG-5' at 619, 3'-GAAG-5' at 1053, 3'-GAAG-5' at 3553, 3'-GAAG-5' at 3776.
  2. negative strand, positive direction, looking for DCE SIc: 3'-GAAG-5', 24, 3'-GAAG-5' at 48, 3'-GAAG-5' at 209, 3'-GAAG-5' at 232, 3'-GAAG-5' at 559, 3'-GAAG-5' at 643, 3'-GAAG-5' at 727, 3'-GAAG-5' at 768, 3'-GAAG-5' at 861, 3'-GAAG-5' at 961, 3'-GAAG-5' at 1063, 3'-GAAG-5' at 1231, 3'-GAAG-5' at 1594, 3'-GAAG-5' at 1633, 3'-GAAG-5' at 2192, 3'-GAAG-5' at 2748, 3'-GAAG-5' at 2784, 3'-GAAG-5' at 3216, 3'-GAAG-5' at 3667, 3'-GAAG-5' at 3762, 3'-GAAG-5' at 3851, 3'-GAAG-5' at 3871, 3'-GAAG-5' at 4197, 3'-GAAG-5' at 4248, 3'-GAAG-5' at 4263.
  3. positive strand, negative direction, looking for DCE SIc: 3'-GAAG-5', 16, 3'-GAAG-5' at 81, 3'-GAAG-5' at 132, 3'-GAAG-5' at 241, 3'-GAAG-5' at 331, 3'-GAAG-5' at 367, 3'-GAAG-5' at 1555, 3'-GAAG-5' at 1655, 3'-GAAG-5' at 2557, 3'-GAAG-5' at 2595, 3'-GAAG-5' at 2730, 3'-GAAG-5' at 2811, 3'-GAAG-5' at 2828, 3'-GAAG-5' at 3407, 3'-GAAG-5' at 3610, 3'-GAAG-5' at 3909, 3'-GAAG-5' at 3936.
  4. positive strand, positive direction, looking for DCE SIc: 3'-GAAG-5', 30, 3'-GAAG-5' at 456, 3'-GAAG-5' at 592, 3'-GAAG-5' at 676, 3'-GAAG-5' at 733, 3'-GAAG-5' at 760, 3'-GAAG-5' at 828, 3'-GAAG-5' at 928, 3'-GAAG-5' at 1012, 3'-GAAG-5' at 1069, 3'-GAAG-5' at 1153, 3'-GAAG-5' at 1264, 3'-GAAG-5' at 1305, 3'-GAAG-5' at 1332, 3'-GAAG-5' at 1405, 3'-GAAG-5' at 1432, 3'-GAAG-5' at 1516, 3'-GAAG-5' at 1914, 3'-GAAG-5' at 2095, 3'-GAAG-5' at 2107, 3'-GAAG-5' at 2361, 3'-GAAG-5' at 2582, 3'-GAAG-5' at 2947, 3'-GAAG-5' at 3031, 3'-GAAG-5' at 3057, 3'-GAAG-5' at 3247, 3'-GAAG-5' at 3312, 3'-GAAG-5' at 3394, 3'-GAAG-5' at 3994, 3'-GAAG-5' at 4061, 3'-GAAG-5' at 4241.

Downstream core element SII Complements

  1. negative strand, negative direction, looking for DCE SIIc: 3'-GACA-5', 30, 3'-GACA-5' at 394, 3'-GACA-5' at 477, 3'-GACA-5' at 667, 3'-GACA-5' at 801, 3'-GACA-5' at 919, 3'-GACA-5' at 967, 3'-GACA-5' at 1085, 3'-GACA-5' at 1131, 3'-GACA-5' at 1258, 3'-GACA-5' at 1452, 3'-GACA-5' at 1776, 3'-GACA-5' at 1911, 3'-GACA-5' at 2029, 3'-GACA-5' at 2163, 3'-GACA-5' at 2337, 3'-GACA-5' at 2538, 3'-GACA-5' at 2672, 3'-GACA-5' at 3061, 3'-GACA-5' at 3200, 3'-GACA-5' at 3265, 3'-GACA-5' at 3319, 3'-GACA-5' at 3426, 3'-GACA-5' at 3556, 3'-GACA-5' at 3709, 3'-GACA-5' at 3957, 3'-GACA-5' at 3970, 3'-GACA-5' at 4121, 3'-GACA-5' at 4208, 3'-GACA-5' at 4369, 3'-GACA-5' at 4399.
  2. negative strand, positive direction, looking for DCE SIIc: 3'-GACA-5', 15, 3'-GACA-5' at 62, 3'-GACA-5' at 712, 3'-GACA-5' at 1693, 3'-GACA-5' at 1869, 3'-GACA-5' at 1964, 3'-GACA-5' at 2130, 3'-GACA-5' at 2412, 3'-GACA-5' at 2460, 3'-GACA-5' at 2843, 3'-GACA-5' at 3131, 3'-GACA-5' at 3530, 3'-GACA-5' at 3569, 3'-GACA-5' at 3893, 3'-GACA-5' at 3973, 3'-GACA-5' at 4252.
  3. positive strand, negative direction, looking for DCE SIIc: 3'-GACA-5', 17, 3'-GACA-5' at 170, 3'-GACA-5' at 422, 3'-GACA-5' at 559, 3'-GACA-5' at 746, 3'-GACA-5' at 1068, 3'-GACA-5' at 1569, 3'-GACA-5' at 2015, 3'-GACA-5' at 2117, 3'-GACA-5' at 2271, 3'-GACA-5' at 2880, 3'-GACA-5' at 2948, 3'-GACA-5' at 3389, 3'-GACA-5' at 3412, 3'-GACA-5' at 3433, 3'-GACA-5' at 3756, 3'-GACA-5' at 4181, 3'-GACA-5' at 4355.
  4. positive strand, positive direction, looking for DCE SIc: 3'-GAAG-5', 25, 3'-GACA-5' at 98, 3'-GACA-5' at 144, 3'-GACA-5' at 264, 3'-GACA-5' at 816, 3'-GACA-5' at 891, 3'-GACA-5' at 916, 3'-GACA-5' at 991, 3'-GACA-5' at 1729, 3'-GACA-5' at 1860, 3'-GACA-5' at 1998, 3'-GACA-5' at 2074, 3'-GACA-5' at 2182, 3'-GACA-5' at 2250, 3'-GACA-5' at 2260, 3'-GACA-5' at 2308, 3'-GACA-5' at 2342, 3'-GACA-5' at 2925, 3'-GACA-5' at 2931, 3'-GACA-5' at 2957, 3'-GACA-5' at 3349, 3'-GACA-5' at 3390, 3'-GACA-5' at 3434, 3'-GACA-5' at 3617, 3'-GACA-5' at 3622, 3'-GACA-5' at 3640.

Downstream core element SIII Complements

  1. negative strand, negative direction, looking for DCE SIIIc: 3'-TCG-5', 88, 3'-TCG-5' at 35, 3'-TCG-5' at 137, 3'-TCG-5' at 146, 3'-TCG-5' at 185, 3'-TCG-5' at 403, 3'-TCG-5' at 455, 3'-TCG-5' at 500, 3'-TCG-5' at 504, 3'-TCG-5' at 540, 3'-TCG-5' at 676, 3'-TCG-5' at 728, 3'-TCG-5' at 737, 3'-TCG-5' at 778, 3'-TCG-5' at 810, 3'-TCG-5' at 870, 3'-TCG-5' at 895, 3'-TCG-5' at 909, 3'-TCG-5' at 944, 3'-TCG-5' at 976, 3'-TCG-5' at 1036, 3'-TCG-5' at 1061, 3'-TCG-5' at 1140, 3'-TCG-5' at 1194, 3'-TCG-5' at 1235, 3'-TCG-5' at 1267, 3'-TCG-5' at 1327, 3'-TCG-5' at 1367, 3'-TCG-5' at 1486, 3'-TCG-5' at 1497, 3'-TCG-5' at 1611, 3'-TCG-5' at 1678, 3'-TCG-5' at 1785, 3'-TCG-5' at 1888, 3'-TCG-5' at 1920, 3'-TCG-5' at 1969, 3'-TCG-5' at 1980, 3'-TCG-5' at 2005, 3'-TCG-5' at 2019, 3'-TCG-5' at 2094, 3'-TCG-5' at 2129, 3'-TCG-5' at 2264, 3'-TCG-5' at 2273, 3'-TCG-5' at 2314, 3'-TCG-5' at 2346, 3'-TCG-5' at 2406, 3'-TCG-5' at 2431, 3'-TCG-5' at 2472, 3'-TCG-5' at 2478, 3'-TCG-5' at 2650, 3'-TCG-5' at 2681, 3'-TCG-5' at 2741, 3'-TCG-5' at 2766, 3'-TCG-5' at 2780, 3'-TCG-5' at 2915, 3'-TCG-5' at 3032, 3'-TCG-5' at 3070, 3'-TCG-5' at 3105, 3'-TCG-5' at 3124, 3'-TCG-5' at 3177, 3'-TCG-5' at 3204, 3'-TCG-5' at 3209, 3'-TCG-5' at 3269, 3'-TCG-5' at 3294, 3'-TCG-5' at 3309, 3'-TCG-5' at 3370, 3'-TCG-5' at 3494, 3'-TCG-5' at 3646, 3'-TCG-5' at 3682, 3'-TCG-5' at 3694, 3'-TCG-5' at 3701, 3'-TCG-5' at 3726, 3'-TCG-5' at 3731, 3'-TCG-5' at 3773, 3'-TCG-5' at 3838, 3'-TCG-5' at 3845, 3'-TCG-5' at 3899, 3'-TCG-5' at 3912, 3'-TCG-5' at 4014, 3'-TCG-5' at 4033, 3'-TCG-5' at 4130, 3'-TCG-5' at 4184, 3'-TCG-5' at 4229, 3'-TCG-5' at 4261, 3'-TCG-5' at 4296, 3'-TCG-5' at 4321, 3'-TCG-5' at 4345, 3'-TCG-5' at 4411, 3'-TCG-5' at 4439.
  2. negative strand, positive direction, looking for DCE SIIIc: 3'-TCG-5', 26, 3'-TCG-5' at 77, 3'-TCG-5' at 457, 3'-TCG-5' at 537, 3'-TCG-5' at 593, 3'-TCG-5' at 688, 3'-TCG-5' at 761, 3'-TCG-5' at 1013, 3'-TCG-5' at 1108, 3'-TCG-5' at 1154, 3'-TCG-5' at 1181, 3'-TCG-5' at 1306, 3'-TCG-5' at 1390, 3'-TCG-5' at 1406, 3'-TCG-5' at 1490, 3'-TCG-5' at 1517, 3'-TCG-5' at 1528, 3'-TCG-5' at 1687, 3'-TCG-5' at 1713, 3'-TCG-5' at 1750, 3'-TCG-5' at 1915, 3'-TCG-5' at 1927, 3'-TCG-5' at 2091, 3'-TCG-5' at 3272, 3'-TCG-5' at 3283, 3'-TCG-5' at 3509, 3'-TCG-5' at 3985.
  3. positive strand, negative direction, looking for DCE SIIIc: 3'-TCG-5', 11, 3'-TCG-5' at 157, 3'-TCG-5' at 720, 3'-TCG-5' at 838, 3'-TCG-5' at 1065, 3'-TCG-5' at 1446, 3'-TCG-5' at 2453, 3'-TCG-5' at 2709, 3'-TCG-5' at 3501, 3'-TCG-5' at 3595, 3'-TCG-5' at 3813, 3'-TCG-5' at 4289.
  4. positive strand, positive direction, looking for DCE SIIIc: 3'-TCG-5', 109, 3'-TCG-5' at 64, 3'-TCG-5' at 329, 3'-TCG-5' at 335, 3'-TCG-5' at 339, 3'-TCG-5' at 383, 3'-TCG-5' at 427, 3'-TCG-5' at 431, 3'-TCG-5' at 473, 3'-TCG-5' at 511, 3'-TCG-5' at 533, 3'-TCG-5' at 560, 3'-TCG-5' at 601, 3'-TCG-5' at 613, 3'-TCG-5' at 617, 3'-TCG-5' at 623, 3'-TCG-5' at 634, 3'-TCG-5' at 644, 3'-TCG-5' at 692, 3'-TCG-5' at 718, 3'-TCG-5' at 728, 3'-TCG-5' at 769, 3'-TCG-5' at 785, 3'-TCG-5' at 831, 3'-TCG-5' at 837, 3'-TCG-5' at 853, 3'-TCG-5' at 931, 3'-TCG-5' at 937, 3'-TCG-5' at 953, 3'-TCG-5' at 1037, 3'-TCG-5' at 1054, 3'-TCG-5' at 1057, 3'-TCG-5' at 1064, 3'-TCG-5' at 1105, 3'-TCG-5' at 1112, 3'-TCG-5' at 1121, 3'-TCG-5' at 1127, 3'-TCG-5' at 1145, 3'-TCG-5' at 1205, 3'-TCG-5' at 1232, 3'-TCG-5' at 1267, 3'-TCG-5' at 1271, 3'-TCG-5' at 1288, 3'-TCG-5' at 1341, 3'-TCG-5' at 1348, 3'-TCG-5' at 1357, 3'-TCG-5' at 1363, 3'-TCG-5' at 1441, 3'-TCG-5' at 1448, 3'-TCG-5' at 1457, 3'-TCG-5' at 1463, 3'-TCG-5' at 1507, 3'-TCG-5' at 1532, 3'-TCG-5' at 1540, 3'-TCG-5' at 1595, 3'-TCG-5' at 1603, 3'-TCG-5' at 1625, 3'-TCG-5' at 1634, 3'-TCG-5' at 1678, 3'-TCG-5' at 2005, 3'-TCG-5' at 2008, 3'-TCG-5' at 2052, 3'-TCG-5' at 2102, 3'-TCG-5' at 2193, 3'-TCG-5' at 2198, 3'-TCG-5' at 2352, 3'-TCG-5' at 2390, 3'-TCG-5' at 2399, 3'-TCG-5' at 2402, 3'-TCG-5' at 2526, 3'-TCG-5' at 2536, 3'-TCG-5' at 2557, 3'-TCG-5' at 2703, 3'-TCG-5' at 2731, 3'-TCG-5' at 2749, 3'-TCG-5' at 2785, 3'-TCG-5' at 2845, 3'-TCG-5' at 2896, 3'-TCG-5' at 2970, 3'-TCG-5' at 3041, 3'-TCG-5' at 3100, 3'-TCG-5' at 3125, 3'-TCG-5' at 3137, 3'-TCG-5' at 3144, 3'-TCG-5' at 3155, 3'-TCG-5' at 3194, 3'-TCG-5' at 3211, 3'-TCG-5' at 3217, 3'-TCG-5' at 3223, 3'-TCG-5' at 3239, 3'-TCG-5' at 3262, 3'-TCG-5' at 3513, 3'-TCG-5' at 3518, 3'-TCG-5' at 3598, 3'-TCG-5' at 3668, 3'-TCG-5' at 3691, 3'-TCG-5' at 3701, 3'-TCG-5' at 3720, 3'-TCG-5' at 3723, 3'-TCG-5' at 3737, 3'-TCG-5' at 3763, 3'-TCG-5' at 3775, 3'-TCG-5' at 3808, 3'-TCG-5' at 3895, 3'-TCG-5' at 3997, 3'-TCG-5' at 4023, 3'-TCG-5' at 4026, 3'-TCG-5' at 4052, 3'-TCG-5' at 4279.

Downstream core element SI Inverse complements

  1. looking for DCE SIci: 3'-GAAG-5', same as the complements.

Downstream core element SII Inverse complements

  1. negative strand, negative direction, looking for DCE SIIci: 3'-ACAG-5', 13, 3'-ACAG-5' at 478, 3'-ACAG-5' at 920, 3'-ACAG-5' at 1086, 3'-ACAG-5' at 1221, 3'-ACAG-5' at 2030, 3'-ACAG-5' at 2164, 3'-ACAG-5' at 2985, 3'-ACAG-5' at 3201, 3'-ACAG-5' at 3320, 3'-ACAG-5' at 3622, 3'-ACAG-5' at 3832, 3'-ACAG-5' at 4209, 3'-ACAG-5' at 4370.
  2. negative strand, positive direction, looking for DCE SIIci: 3'-ACAG-5', 28, 3'-ACAG-5' at 63, 3'-ACAG-5' at 156, 3'-ACAG-5' at 364, 3'-ACAG-5' at 551, 3'-ACAG-5' at 633, 3'-ACAG-5' at 717, 3'-ACAG-5' at 1053, 3'-ACAG-5' at 1823, 3'-ACAG-5' at 1965, 3'-ACAG-5' at 2124, 3'-ACAG-5' at 2131, 3'-ACAG-5' at 2413, 3'-ACAG-5' at 2461, 3'-ACAG-5' at 2651, 3'-ACAG-5' at 2836, 3'-ACAG-5' at 2844, 3'-ACAG-5' at 3099, 3'-ACAG-5' at 3132, 3'-ACAG-5' at 3178, 3'-ACAG-5' at 3193, 3'-ACAG-5' at 3210, 3'-ACAG-5' at 3412, 3'-ACAG-5' at 3570, 3'-ACAG-5' at 3635, 3'-ACAG-5' at 3860, 3'-ACAG-5' at 3894, 3'-ACAG-5' at 3974, 3'-ACAG-5' at 4069.
  3. positive strand, negative direction, looking for DCE SIIci: 3'-ACAG-5', 25, 3'-ACAG-5' at 12, 3'-ACAG-5' at 167, 3'-ACAG-5' at 288, 3'-ACAG-5' at 296, 3'-ACAG-5' at 423, 3'-ACAG-5' at 519, 3'-ACAG-5' at 560, 3'-ACAG-5' at 906, 3'-ACAG-5' at 1072, 3'-ACAG-5' at 1117, 3'-ACAG-5' at 1566, 3'-ACAG-5' at 2016, 3'-ACAG-5' at 2118, 3'-ACAG-5' at 2272, 3'-ACAG-5' at 2442, 3'-ACAG-5' at 2513, 3'-ACAG-5' at 2688, 3'-ACAG-5' at 2777, 3'-ACAG-5' at 2877, 3'-ACAG-5' at 3671, 3'-ACAG-5' at 3693, 3'-ACAG-5' at 3725, 3'-ACAG-5' at 3916, 3'-ACAG-5' at 4197, 3'-ACAG-5' at 4356.
  4. positive strand, positive direction, looking for DCE SIIci: 3'-ACAG-5', 20, 3'-ACAG-5' at 81, 3'-ACAG-5' at 99, 3'-ACAG-5' at 267, 3'-ACAG-5' at 892, 3'-ACAG-5' at 992, 3'-ACAG-5' at 1730, 3'-ACAG-5' at 1861, 3'-ACAG-5' at 1999, 3'-ACAG-5' at 2077, 3'-ACAG-5' at 2171, 3'-ACAG-5' at 2309, 3'-ACAG-5' at 2465, 3'-ACAG-5' at 2926, 3'-ACAG-5' at 3003, 3'-ACAG-5' at 3052, 3'-ACAG-5' at 3391, 3'-ACAG-5' at 3576, 3'-ACAG-5' at 3618, 3'-ACAG-5' at 3744, 3'-ACAG-5' at 3951.

Downstream core element SIII Inverse complements

  1. negative strand, negative direction, looking for DCE SIIIci: 3'-GCT-5', 23, 3'-GCT-5' at 310, 3'-GCT-5' at 434, 3'-GCT-5' at 448, 3'-GCT-5' at 492, 3'-GCT-5' at 571, 3'-GCT-5' at 707, 3'-GCT-5' at 721, 3'-GCT-5' at 911, 3'-GCT-5' at 1039, 3'-GCT-5' at 1066, 3'-GCT-5' at 1155, 3'-GCT-5' at 1181, 3'-GCT-5' at 1189, 3'-GCT-5' at 1330, 3'-GCT-5' at 1553, 3'-GCT-5' at 1983, 3'-GCT-5' at 2013, 3'-GCT-5' at 2155, 3'-GCT-5' at 2409, 3'-GCT-5' at 3231, 3'-GCT-5' at 3814, 3'-GCT-5' at 3875, 3'-GCT-5' at 4241.
  2. negative strand, positive direction, looking for DCE SIIIci: 3'-GCT-5', 87, 3'-GCT-5' at 3, 3'-GCT-5' at 10, 3'-GCT-5' at 262, 3'-GCT-5' at 275, 3'-GCT-5' at 384, 3'-GCT-5' at 415, 3'-GCT-5' at 479, 3'-GCT-5' at 518, 3'-GCT-5' at 528, 3'-GCT-5' at 602, 3'-GCT-5' at 652, 3'-GCT-5' at 693, 3'-GCT-5' at 737, 3'-GCT-5' at 777, 3'-GCT-5' at 838, 3'-GCT-5' at 938, 3'-GCT-5' at 1029, 3'-GCT-5' at 1093, 3'-GCT-5' at 1106, 3'-GCT-5' at 1113, 3'-GCT-5' at 1177, 3'-GCT-5' at 1190, 3'-GCT-5' at 1274, 3'-GCT-5' at 1342, 3'-GCT-5' at 1349, 3'-GCT-5' at 1442, 3'-GCT-5' at 1449, 3'-GCT-5' at 1533, 3'-GCT-5' at 1576, 3'-GCT-5' at 1651, 3'-GCT-5' at 1727, 3'-GCT-5' at 1734, 3'-GCT-5' at 1777, 3'-GCT-5' at 1817, 3'-GCT-5' at 1882, 3'-GCT-5' at 1907, 3'-GCT-5' at 1973, 3'-GCT-5' at 2043, 3'-GCT-5' at 2046, 3'-GCT-5' at 2053, 3'-GCT-5' at 2056, 3'-GCT-5' at 2089, 3'-GCT-5' at 2093, 3'-GCT-5' at 2155, 3'-GCT-5' at 2161, 3'-GCT-5' at 2194, 3'-GCT-5' at 2318, 3'-GCT-5' at 2368, 3'-GCT-5' at 2403, 3'-GCT-5' at 2435, 3'-GCT-5' at 2504, 3'-GCT-5' at 2695, 3'-GCT-5' at 2732, 3'-GCT-5' at 2750, 3'-GCT-5' at 2753, 3'-GCT-5' at 2768, 3'-GCT-5' at 2786, 3'-GCT-5' at 2808, 3'-GCT-5' at 2846, 3'-GCT-5' at 2885, 3'-GCT-5' at 2913, 3'-GCT-5' at 2971, 3'-GCT-5' at 2976, 3'-GCT-5' at 3119, 3'-GCT-5' at 3151, 3'-GCT-5' at 3195, 3'-GCT-5' at 3227, 3'-GCT-5' at 3240, 3'-GCT-5' at 3263, 3'-GCT-5' at 3274, 3'-GCT-5' at 3307, 3'-GCT-5' at 3347, 3'-GCT-5' at 3368, 3'-GCT-5' at 3420, 3'-GCT-5' at 3481, 3'-GCT-5' at 3519, 3'-GCT-5' at 3524, 3'-GCT-5' at 3586, 3'-GCT-5' at 3638, 3'-GCT-5' at 3696, 3'-GCT-5' at 3724, 3'-GCT-5' at 3776, 3'-GCT-5' at 3983, 3'-GCT-5' at 3987, 3'-GCT-5' at 3992, 3'-GCT-5' at 4027, 3'-GCT-5' at 4175.
  3. positive strand, negative direction, looking for DCE SIIIci: 3'-GCT-5', 78, 3'-GCT-5' at 138, 3'-GCT-5' at 147, 3'-GCT-5' at 335, 3'-GCT-5' at 385, 3'-GCT-5' at 598, 3'-GCT-5' at 658, 3'-GCT-5' at 779, 3'-GCT-5' at 811, 3'-GCT-5' at 823, 3'-GCT-5' at 840, 3'-GCT-5' at 890, 3'-GCT-5' at 977, 3'-GCT-5' at 989, 3'-GCT-5' at 1006, 3'-GCT-5' at 1109, 3'-GCT-5' at 1122, 3'-GCT-5' at 1268, 3'-GCT-5' at 1280, 3'-GCT-5' at 1448, 3'-GCT-5' at 1462, 3'-GCT-5' at 1487, 3'-GCT-5' at 1498, 3'-GCT-5' at 1744, 3'-GCT-5' at 1754, 3'-GCT-5' at 1767, 3'-GCT-5' at 1798, 3'-GCT-5' at 1843, 3'-GCT-5' at 1889, 3'-GCT-5' at 1906, 3'-GCT-5' at 1921, 3'-GCT-5' at 1970, 3'-GCT-5' at 2067, 3'-GCT-5' at 2107, 3'-GCT-5' at 2130, 3'-GCT-5' at 2202, 3'-GCT-5' at 2224, 3'-GCT-5' at 2324, 3'-GCT-5' at 2347, 3'-GCT-5' at 2359, 3'-GCT-5' at 2376, 3'-GCT-5' at 2529, 3'-GCT-5' at 2560, 3'-GCT-5' at 2682, 3'-GCT-5' at 2694, 3'-GCT-5' at 2711, 3'-GCT-5' at 2742, 3'-GCT-5' at 2896, 3'-GCT-5' at 2933, 3'-GCT-5' at 3006, 3'-GCT-5' at 3033, 3'-GCT-5' at 3039, 3'-GCT-5' at 3052, 3'-GCT-5' at 3083, 3'-GCT-5' at 3106, 3'-GCT-5' at 3178, 3'-GCT-5' at 3210, 3'-GCT-5' at 3222, 3'-GCT-5' at 3263, 3'-GCT-5' at 3398, 3'-GCT-5' at 3580, 3'-GCT-5' at 3647, 3'-GCT-5' at 3702, 3'-GCT-5' at 3707, 3'-GCT-5' at 3717, 3'-GCT-5' at 3774, 3'-GCT-5' at 3862, 3'-GCT-5' at 3955, 3'-GCT-5' at 3961, 3'-GCT-5' at 3992, 3'-GCT-5' at 4112, 3'-GCT-5' at 4131, 3'-GCT-5' at 4143, 3'-GCT-5' at 4185, 3'-GCT-5' at 4255, 3'-GCT-5' at 4262, 3'-GCT-5' at 4274, 3'-GCT-5' at 4291, 3'-GCT-5' at 4402.
  4. positive strand, positive direction, looking for DCE SIIIci: 3'-GCT-5', 36, 3'-GCT-5' at 162, 3'-GCT-5' at 242, 3'-GCT-5' at 308, 3'-GCT-5' at 360, 3'-GCT-5' at 429, 3'-GCT-5' at 555, 3'-GCT-5' at 576, 3'-GCT-5' at 639, 3'-GCT-5' at 766, 3'-GCT-5' at 790, 3'-GCT-5' at 851, 3'-GCT-5' at 896, 3'-GCT-5' at 951, 3'-GCT-5' at 996, 3'-GCT-5' at 1059, 3'-GCT-5' at 1080, 3'-GCT-5' at 1101, 3'-GCT-5' at 1155, 3'-GCT-5' at 1164, 3'-GCT-5' at 1227, 3'-GCT-5' at 1346, 3'-GCT-5' at 1379, 3'-GCT-5' at 1446, 3'-GCT-5' at 1479, 3'-GCT-5' at 1563, 3'-GCT-5' at 1584, 3'-GCT-5' at 1623, 3'-GCT-5' at 1665, 3'-GCT-5' at 1835, 3'-GCT-5' at 1919, 3'-GCT-5' at 1962, 3'-GCT-5' at 2215, 3'-GCT-5' at 2357, 3'-GCT-5' at 2804, 3'-GCT-5' at 3799, 3'-GCT-5' at 4277.

Downstream core element SI Inverses

  1. looking for DCE SIi: 3'-CTTC-5', same as the direct.

Downstream core element SII Inverses

  1. negative strand, negative direction, looking for DCE SIIi: 3'-TGTC-5', 25, 3'-TGTC-5' at 12, 3'-TGTC-5' at 167, 3'-TGTC-5' at 288, 3'-TGTC-5' at 296, 3'-TGTC-5' at 423, 3'-TGTC-5' at 519, 3'-TGTC-5' at 560, 3'-TGTC-5' at 906, 3'-TGTC-5' at 1072, 3'-TGTC-5' at 1117, 3'-TGTC-5' at 1566, 3'-TGTC-5' at 2016, 3'-TGTC-5' at 2118, 3'-TGTC-5' at 2272, 3'-TGTC-5' at 2442, 3'-TGTC-5' at 2513, 3'-TGTC-5' at 2688, 3'-TGTC-5' at 2777, 3'-TGTC-5' at 2877, 3'-TGTC-5' at 3671, 3'-TGTC-5' at 3693, 3'-TGTC-5' at 3725, 3'-TGTC-5' at 3916, 3'-TGTC-5' at 4197, 3'-TGTC-5' at 4356.
  2. negative strand, positive direction, looking for DCE SIIi: 3'-TGTC-5', 20, 3'-TGTC-5' at 81, 3'-TGTC-5' at 99, 3'-TGTC-5' at 267, 3'-TGTC-5' at 892, 3'-TGTC-5' at 992, 3'-TGTC-5' at 1730, 3'-TGTC-5' at 1861, 3'-TGTC-5' at 1999, 3'-TGTC-5' at 2077, 3'-TGTC-5' at 2171, 3'-TGTC-5' at 2309, 3'-TGTC-5' at 2465, 3'-TGTC-5' at 2926, 3'-TGTC-5' at 3003, 3'-TGTC-5' at 3052, 3'-TGTC-5' at 3391, 3'-TGTC-5' at 3576, 3'-TGTC-5' at 3618, 3'-TGTC-5' at 3744, 3'-TGTC-5' at 3951.
  3. positive strand, negative direction, looking for DCE SIIi: 3'-TGTC-5', 13, 3'-TGTC-5' at 478, 3'-TGTC-5' at 920, 3'-TGTC-5' at 1086, 3'-TGTC-5' at 1221, 3'-TGTC-5' at 2030, 3'-TGTC-5' at 2164, 3'-TGTC-5' at 2985, 3'-TGTC-5' at 3201, 3'-TGTC-5' at 3320, 3'-TGTC-5' at 3622, 3'-TGTC-5' at 3832, 3'-TGTC-5' at 4209, 3'-TGTC-5' at 4370.
  4. positive strand, positive direction, looking for DCE SIIi: 3'-TGTC-5', 28, 3'-TGTC-5' at 63, 3'-TGTC-5' at 156, 3'-TGTC-5' at 364, 3'-TGTC-5' at 551, 3'-TGTC-5' at 633, 3'-TGTC-5' at 717, 3'-TGTC-5' at 1053, 3'-TGTC-5' at 1823, 3'-TGTC-5' at 1965, 3'-TGTC-5' at 2124, 3'-TGTC-5' at 2131, 3'-TGTC-5' at 2413, 3'-TGTC-5' at 2461, 3'-TGTC-5' at 2651, 3'-TGTC-5' at 2836, 3'-TGTC-5' at 2844, 3'-TGTC-5' at 3099, 3'-TGTC-5' at 3132, 3'-TGTC-5' at 3178, 3'-TGTC-5' at 3193, 3'-TGTC-5' at 3210, 3'-TGTC-5' at 3412, 3'-TGTC-5' at 3570, 3'-TGTC-5' at 3635, 3'-TGTC-5' at 3860, 3'-TGTC-5' at 3894, 3'-TGTC-5' at 3974, 3'-TGTC-5' at 4069.

Downstream core element SIII Inverses

  1. negative strand, negative direction, looking for DCE SIIIi: 3'-CGA-5', 78, 3'-CGA-5' at 138, 3'-CGA-5' at 147, 3'-CGA-5' at 335, 3'-CGA-5' at 385, 3'-CGA-5' at 598, 3'-CGA-5' at 658, 3'-CGA-5' at 779, 3'-CGA-5' at 811, 3'-CGA-5' at 823, 3'-CGA-5' at 840, 3'-CGA-5' at 890, 3'-CGA-5' at 977, 3'-CGA-5' at 989, 3'-CGA-5' at 1006, 3'-CGA-5' at 1109, 3'-CGA-5' at 1122, 3'-CGA-5' at 1268, 3'-CGA-5' at 1280, 3'-CGA-5' at 1448, 3'-CGA-5' at 1462, 3'-CGA-5' at 1487, 3'-CGA-5' at 1498, 3'-CGA-5' at 1744, 3'-CGA-5' at 1754, 3'-CGA-5' at 1767, 3'-CGA-5' at 1798, 3'-CGA-5' at 1843, 3'-CGA-5' at 1889, 3'-CGA-5' at 1906, 3'-CGA-5' at 1921, 3'-CGA-5' at 1970, 3'-CGA-5' at 2067, 3'-CGA-5' at 2107, 3'-CGA-5' at 2130, 3'-CGA-5' at 2202, 3'-CGA-5' at 2224, 3'-CGA-5' at 2324, 3'-CGA-5' at 2347, 3'-CGA-5' at 2359, 3'-CGA-5' at 2376, 3'-CGA-5' at 2529, 3'-CGA-5' at 2560, 3'-CGA-5' at 2682, 3'-CGA-5' at 2694, 3'-CGA-5' at 2711, 3'-CGA-5' at 2742, 3'-CGA-5' at 2896, 3'-CGA-5' at 2933, 3'-CGA-5' at 3006, 3'-CGA-5' at 3033, 3'-CGA-5' at 3039, 3'-CGA-5' at 3052, 3'-CGA-5' at 3083, 3'-CGA-5' at 3106, 3'-CGA-5' at 3178, 3'-CGA-5' at 3210, 3'-CGA-5' at 3222, 3'-CGA-5' at 3263, 3'-CGA-5' at 3398, 3'-CGA-5' at 3580, 3'-CGA-5' at 3647, 3'-CGA-5' at 3702, 3'-CGA-5' at 3707, 3'-CGA-5' at 3717, 3'-CGA-5' at 3774, 3'-CGA-5' at 3862, 3'-CGA-5' at 3955, 3'-CGA-5' at 3961, 3'-CGA-5' at 3992, 3'-CGA-5' at 4112, 3'-CGA-5' at 4131, 3'-CGA-5' at 4143, 3'-CGA-5' at 4185, 3'-CGA-5' at 4255, 3'-CGA-5' at 4262, 3'-CGA-5' at 4274, 3'-CGA-5' at 4291, 3'-CGA-5' at 4402.
  2. negative strand, positive direction, looking for DCE SIIIi: 3'-CGA-5', 36, 3'-CGA-5' at 162, 3'-CGA-5' at 242, 3'-CGA-5' at 308, 3'-CGA-5' at 360, 3'-CGA-5' at 429, 3'-CGA-5' at 555, 3'-CGA-5' at 576, 3'-CGA-5' at 639, 3'-CGA-5' at 766, 3'-CGA-5' at 790, 3'-CGA-5' at 851, 3'-CGA-5' at 896, 3'-CGA-5' at 951, 3'-CGA-5' at 996, 3'-CGA-5' at 1059, 3'-CGA-5' at 1080, 3'-CGA-5' at 1101, 3'-CGA-5' at 1155, 3'-CGA-5' at 1164, 3'-CGA-5' at 1227, 3'-CGA-5' at 1346, 3'-CGA-5' at 1379, 3'-CGA-5' at 1446, 3'-CGA-5' at 1479, 3'-CGA-5' at 1563, 3'-CGA-5' at 1584, 3'-CGA-5' at 1623, 3'-CGA-5' at 1665, 3'-CGA-5' at 1835, 3'-CGA-5' at 1919, 3'-CGA-5' at 1962, 3'-CGA-5' at 2215, 3'-CGA-5' at 2357, 3'-CGA-5' at 2804, 3'-CGA-5' at 3799, 3'-CGA-5' at 4277.
  3. positive strand, negative direction, looking for DCE SIIIi: 3'-CGA-5', 24, 3'-CGA-5' at 310, 3'-CGA-5' at 434, 3'-CGA-5' at 448, 3'-CGA-5' at 492, 3'-CGA-5' at 571, 3'-CGA-5' at 707, 3'-CGA-5' at 721, 3'-CGA-5' at 911, 3'-CGA-5' at 1039, 3'-CGA-5' at 1066, 3'-CGA-5' at 1155, 3'-CGA-5' at 1181, 3'-CGA-5' at 1189, 3'-CGA-5' at 1330, 3'-CGA-5' at 1553, 3'-CGA-5' at 1983, 3'-CGA-5' at 2013, 3'-CGA-5' at 2155, 3'-CGA-5' at 2409, 3'-CGA-5' at 3231, 3'-CGA-5' at 3814, 3'-CGA-5' at 3875, 3'-CGA-5' at 4241.
  4. positive strand, positive direction, looking for DCE SIIIi: 3'-CGA-5', 87, 3'-CGA-5' at 3, 3'-CGA-5' at 10, 3'-CGA-5' at 262, 3'-CGA-5' at 275, 3'-CGA-5' at 384, 3'-CGA-5' at 415, 3'-CGA-5' at 479, 3'-CGA-5' at 518, 3'-CGA-5' at 528, 3'-CGA-5' at 602, 3'-CGA-5' at 652, 3'-CGA-5' at 693, 3'-CGA-5' at 737, 3'-CGA-5' at 777, 3'-CGA-5' at 838, 3'-CGA-5' at 938, 3'-CGA-5' at 1029, 3'-CGA-5' at 1093, 3'-CGA-5' at 1106, 3'-CGA-5' at 1113, 3'-CGA-5' at 1177, 3'-CGA-5' at 1190, 3'-CGA-5' at 1274, 3'-CGA-5' at 1342, 3'-CGA-5' at 1349, 3'-CGA-5' at 1442, 3'-CGA-5' at 1449, 3'-CGA-5' at 1533, 3'-CGA-5' at 1576, 3'-CGA-5' at 1651, 3'-CGA-5' at 1727, 3'-CGA-5' at 1734, 3'-CGA-5' at 1777, 3'-CGA-5' at 1817, 3'-CGA-5' at 1882, 3'-CGA-5' at 1907, 3'-CGA-5' at 1973, 3'-CGA-5' at 2043, 3'-CGA-5' at 2046, 3'-CGA-5' at 2053, 3'-CGA-5' at 2056, 3'-CGA-5' at 2089, 3'-CGA-5' at 2093, 3'-CGA-5' at 2155, 3'-CGA-5' at 2161, 3'-CGA-5' at 2194, 3'-CGA-5' at 2318, 3'-CGA-5' at 2368, 3'-CGA-5' at 2403, 3'-CGA-5' at 2435, 3'-CGA-5' at 2504, 3'-CGA-5' at 2695, 3'-CGA-5' at 2732, 3'-CGA-5' at 2750, 3'-CGA-5' at 2753, 3'-CGA-5' at 2768, 3'-CGA-5' at 2786, 3'-CGA-5' at 2808, 3'-CGA-5' at 2846, 3'-CGA-5' at 2885, 3'-CGA-5' at 2913, 3'-CGA-5' at 2971, 3'-CGA-5' at 2976, 3'-CGA-5' at 3119, 3'-CGA-5' at 3151, 3'-CGA-5' at 3195, 3'-CGA-5' at 3227, 3'-CGA-5' at 3240, 3'-CGA-5' at 3263, 3'-CGA-5' at 3274, 3'-CGA-5' at 3307, 3'-CGA-5' at 3347, 3'-CGA-5' at 3368, 3'-CGA-5' at 3420, 3'-CGA-5' at 3481, 3'-CGA-5' at 3519, 3'-CGA-5' at 3524, 3'-CGA-5' at 3586, 3'-CGA-5' at 3638, 3'-CGA-5' at 3696, 3'-CGA-5' at 3724, 3'-CGA-5' at 3776, 3'-CGA-5' at 3983, 3'-CGA-5' at 3987, 3'-CGA-5' at 3992, 3'-CGA-5' at 4027, 3'-CGA-5' at 4175.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ Wonderfool (25 March 2006). "downstream". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2013-06-28.
  2. ↑ Poccil (20 October 2004). "core". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2013-06-28.
  3. ↑ SemperBlotto (5 August 2012). "core". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2013-06-28.
  4. ↑ 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 Dong-Hoon Lee, Naum Gershenzon, Malavika Gupta, Ilya P. Ioshikhes, Danny Reinberg and Brian A. Lewis (November 2005). "Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1". Molecular and Cellular Biology. 25 (21): 9674–86. doi:10.1128/MCB.25.21.9674-9686.2005. PMID 16227614. Retrieved 2010-10-23.
  5. ↑ Stephen T. Smale and James T. Kadonaga (July 2003). "The RNA Polymerase II Core Promoter" (PDF). Annual Review of Biochemistry. 72 (1): 449–79. doi:10.1146/annurev.biochem.72.121801.161520. PMID 12651739. Retrieved 2012-05-07.
  6. ↑ Thomas W. Burke and James T. Kadonaga (November 15, 1997). "The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila". Genes & Development. 11 (22): 3020–31. doi:10.1101/gad.11.22.3020. PMC 316699. PMID 9367984.
  7. ↑ Gillian E. Chalkley and C. Peter Verrijzer (September 1, 1999). "DNA binding site selection by RNA polymerase II TAFs: a TAFII250-TAFII150 complex recognizes the Initiator" (PDF). The EMBO Journal. 18 (17): 4835–45. PMID 10469661. Retrieved 2012-04-26.
  8. ↑ S. T. Smale (1997). "Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes". Biochim. Biophys. Acta. 1351: 73–88. |access-date= requires |url= (help)
  9. ↑ 9.0 9.1 Marketa J. Zvelebil, Jeremy O. Baum (2008). Dom Holdsworth, ed. Understanding bioinformatics. New York: Garland Science. p. 772. ISBN 978-0815340249.

Further reading

External links

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